This is a static file that requires getting advanced genotype images and statistic, this can be functional for each accession by editing your clone name in the raw file.
Load required packages
tidyverse, readr, stringr, readxl, magick, ggplot2 and set
your working directory, in my case, working directory is intact
library(tidyverse)
library(readr)
library(readxl)
library(magick)
library(ggplot2)
library(knitr)
getwd()
## [1] "/home/cirec/Desktop/git_workspace/RMKRDpRCT"
The data we will be working with, in our working directory, and also select the list of genotypes in our data, Advancement sub unit.
raw_data <- read_excel("tables/21.GS.C4.AYT.45.IB_Selections.xls", sheet = "Advancement")
get_list_of_accession <- function(){
x <- raw_data$Genotype
return(x)
}
get_list_of_accession()
## [1] "TMS19F1219P0180" "TMS19F1011P0025" "TMS19F1210P0006" "TMS19F1219P0089"
## [5] "TMS19F1194P0076" "TMS19F1224P0002" "TMS19F1371P0025" "TMS19F1225P0010"
## [9] "TMS19F1219P0003" "TMS19F1194P0103"
This chunk of code will be edited at intervals to render a different accession
get_selected_genotype <- function(){
return(get_list_of_accession()[[4]])
}
get_selected_genotype()
## [1] "TMS19F1219P0089"
Get an overview of all the images, we will be using in our code, I am only accessing the first 6 images of over 180 images.
## [1] "2022-21.GS.C4.AYT.45.IB-rep1-IITA-TMS-IBA000070_108_Photos_1_2022-06-29-09-16-58.jpg"
## [2] "2022-21.GS.C4.AYT.45.IB-rep1-IITA-TMS-IBA000070_108_Photos_2_2022-06-29-09-17-10.jpg"
## [3] "2022-21.GS.C4.AYT.45.IB-rep1-IITA-TMS-IBA000070_108_Photos_3_2022-06-29-09-27-07.jpg"
## [4] "2022-21.GS.C4.AYT.45.IB-rep1-IITA-TMS-IBA070593_141_Photos_1_2022-06-29-10-42-22.jpg"
## [5] "2022-21.GS.C4.AYT.45.IB-rep1-IITA-TMS-IBA070593_141_Photos_2_2022-06-29-11-33-52.jpg"
## [6] "2022-21.GS.C4.AYT.45.IB-rep1-IITA-TMS-IBA30572_105_Photos_1_2022-06-29-09-03-47.jpg"
Selec all the images with a particular selected genotype.
This chunk of code will render the images in the list, based on the selected clone
This chunk generates a table that will render a summary statistic of the particular selected genotype
| Trait | Value |
|---|---|
| Genotype | TMS19F1219P0089 |
| MCMDS | 1.24 |
| FYLD | 34.32 |
| DYLD | 11.68 |
| DM | 33.93 |
| SI | 149.11 |